# Variant calling without matched normal sample

I have WGS .bam files for 3 patients (tumour and its matched derived model namely organoid) but I don't matched normal sample. If I call variants of each patients (tumour and its matched organoid), how I can use read counts at germline heterozygous positions estimated by GATK 3.2-2 to compensate for the absence of matched normal sample? I heard people use dbsnp VCF instead of the matched normal small variant VCF. But, I don't know start from where? which GATK function does that?

I should mention, Calling SNV and indel in many tools returns vcf but I called copy number by varscan that did not return .vcf output so I am not sure what to do for CNV

If you just want to filter out calls present in dbSNP then use:

java -jar GenomeAnalysisTK.jar \
-T SelectVariants \
-R reference.fasta \
-V patient.vcf \
--discordance dbSNP.vcf \
-o patient.filtered.vcf


--discordance will produce calls not present in dbSNP.

• Thanks a lot @Devon, Calling SNV and indel in many tools returns vcf but I called copy number by varscan that did not return .vcf output, is this command is applicable yet? Mar 14 '19 at 14:49
• It's usually best to mention things like that in your post... I presume this will still work, but I can't say I've ever tried. Mar 14 '19 at 14:56
• software.broadinstitute.org/gatk/documentation/article?id=11682 Mar 18 '19 at 17:54

Here is a clue by scatngs

https://github.com/cancerit/ascatNgs/wiki/Human-reference-files-from-1000-genomes-VCFs

and already calculated file is here

ftp://ftp.sanger.ac.uk/pub/cancer/support-files/CPIB/ascatNgs/Human/GRCh37/

Although installing scatngs itself is a big burden